IRX1

Source: Wikipedia, the free encyclopedia.
IRX1
Identifiers
Gene ontology
Molecular function
Cellular component
Biological process
Sources:Amigo / QuickGO
Ensembl

ENSG00000170549

ENSMUSG00000060969

UniProt

P78414

P81068

RefSeq (mRNA)

NM_024337

NM_010573

RefSeq (protein)

NP_077313

NP_034703

Location (UCSC)Chr 5: 3.6 – 3.6 MbChr 13: 72.11 – 72.11 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Iroquois-class homeodomain protein IRX-1, also known as Iroquois homeobox protein 1, is a

homeodomain and a characteristic IRO sequence motif.[7] Members of this family are known to play numerous roles in early embryo patterning.[5] IRX1 has also been shown to act as a tumor suppressor gene in several forms of cancer.[8][9][10][11]

Role in development

IRX1 is a member of the Iroquois homeobox gene family. Members of this family play multiple roles during pattern formation in embryos of numerous vertebrate and invertebrate species.[5][12] IRO genes are thought to function early in development to define large territories, and again later in development for further patterning specification.[7] Experimental data suggest roles for IRX1 in vertebrates may include development and patterning of lungs, limbs, heart, eyes, and nervous system.[13][14][15][16][17][18]

Gene

Overview

IRX1 is located on the forward DNA strand (see

chromosome 5, from position 3596054 - 3601403 at the 5p15.3 location.[5] The human gene product is a 1858 base pair mRNA with 4 predicted exons in humans.[19] Promoter analysis was performed using El Dorado through the Genomatix software page.[20]
The predicted promoter region spans 1040 base pairs from position 3595468 through 3595468 on the forward strand of chromosome 5.

Gene neighborhood

IRX1 is relatively isolated, with no other protein coding genes found from position 3177835 – 5070004.[5]

Expression

brachyury.[20] Expression data from human, mouse, and developing mouse brains are available though the Allen Brain Atlas.[25]

Protein

Properties and characteristics

The mature IRX1 protein has 480

ExPASy.[31] Bioinformatic analysis of IRX1 with the NetPhos tool predicted 71 potential phosphorylation sites throughout the protein.[32]

Protein Interactions

Potential protein interacting partners for IRX1 were found using computational tools. The STRING database lists nine putative interacting partners supported by text mining evidence, though closer analysis of the results shows little support for most of these predicted interactions.[33] However, it is possible that one of these proteins, CDKN1A, is involved in the predicted regulation of IRX1 by E2F cell cycle regulators.[20][33]

Conservation

Orthologs

IRX1 has a high degree of conservation across vertebrate and invertebrate species. The entire protein is more fully conserved through vertebrate species, while only the homeodomain and IRO motif are conserved in more distant homologs.[12] Homologous sequences were found in species as distantly related to humans as the pig roundworm Ascaris suum, from the family Ascarididae, using BLAST and the ALIGN tool through the San Diego Super Computer Biology Workbench.[26] The following is a table describing the evolutionary conservation of IRX1.

Genus Species Organism Common Name Divergence from Humans (MYA) [34] NCBI Protein Accession Number Sequence Identity [26] Protein Length Common Gene Name
Homo sapiens[30]
 Humans -- NP_077313 100% 480 IRX-1
Pongo abelii[35]
 Sumatran Orangutan 15.7 XP_002815448 99% 480 IRX-1
Bos taurus[36]
 Cattle 94.2 XP_002696496 92.3% 476 IRX-1
Mus musculus[37]
 House Mouse 92.3 NP_034703 91.5% 480 IRX-1
Rattus norvegicus[38]
 Brown rat 92.3 NP_001100801 90.4% 480 IRX-1
Gallus gallus[39]
 Red Junglefowl 296 NP_001025509 72.9% 467 IRX-1
Xenopus tropicalis[40]
 Western clawed frog 371.2 NP_001188351 68% 467 IRX-1
Latimeria chalumnae[41]
 West Indian Ocean coelacanth 441.9 XP_006002089 65.1% 460 Irx-1-A-like isoform X1
Danio rerio[42]
 Zebrafish 400.1 NP_997067 61.1% 426 Irx-1 isoform 1
Taeniopygia guttata[43]
 Zebra finch 296 XP_002189063 59.7% 400 Irx-1-A-like
Astyanax mexicanus[44]
 Mexican tetra 400.1 XP_007254591.1 58% 450 IRX-1
Ophiophagus hannah[45]
 King cobra 296 ETE68928 54.5% 387 Irx-1-A partial
Ovis aries[46]
 Sheep 94.2 XP_004017207 43.3% 260 IRX-1
Condylura cristata[47]
 Star-nosed mole 94.2 XP_004678440 41.7% 342 IRX-1
Branchiostoma floridae[48] Lancelet 713.2 ACF10237.1 35.5% 461 Iroquois A isoform 1
Strongylocentrotus purpuratus[49] Purple sea urchin 742.9 NP_001123285 31.7% 605 Iroquois homeobox A
Ascaris suum[50] Pig roundworm 937.5 F1KXE6 29% 444 IRX-1
Caenorhabditis elegans[51] Nematode roundworm 937.5 NP_492533.2 28.6% 377 IRX-1
Drosophila melanogaster[52] Fruit fly 782.7 NP_524045 27% 717 Araucan isoform A

Paralogs

IRX1 is one of six members of the Iroquois-class homeodomain proteins found in humans:

chromosome 16.[7] It is thought that the genomic organization of IRO genes in conserved gene clusters allows for coregulation and enhancer
sharing during development.

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000170549 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000060969 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ a b c d e "Entrez Gene: iroquois homeobox 1".
  6. S2CID 46509502
    .
  7. ^
    PMID 11532909
    . Retrieved May 17, 2014.
  8. PMID 18559491
    .
  9. PMID 24076275
    .
  10. S2CID 6638457
    .
  11. PMID 23456299
    .
  12. ^
    PMID 19368711
    .
  13. S2CID 38099649
    .
  14. S2CID 142831
    .
  15. S2CID 16857354
    .
  16. S2CID 9655500
    .
  17. PMID 10926765
    .
  18. PMID 23505533
    .
  19. ^ "NCBI Nucleotide: IRX1". Retrieved May 17, 2014.
  20. ^ a b c "El Dorado". Genomatix. Retrieved May 17, 2014.[permanent dead link]
  21. ^ "BioGPS: IRX1". Retrieved 17 May 2014.
  22. ^ a b "GeneCards: IRX1". Retrieved 17 May 2014.
  23. ^ "GEO Profile: IRX1". Retrieved May 17, 2014.
  24. PMID 10080939
    .
  25. ^ "Allen Brain Atlas". Retrieved May 17, 2014.
  26. ^ a b c "IRX1 Analysis". Biology Workbench. San Diego Supercomputing Center- University of California San Diego. Retrieved 8 May 2014.[permanent dead link]
  27. PMID 9336443
    .
  28. ^ "Expasy: Psort". Retrieved 18 May 2014.[permanent dead link]
  29. ^
    PMID 22186017
    .
  30. ^ a b "NCBI Protein: IRX1". Retrieved 18 May 2014.
  31. ^ "ExPASy: Bioinformatics Resource Portal". Retrieved 18 May 2014.
  32. ^ "NetPhos". Retrieved 18 May 2014.
  33. ^ a b "STRING Database". Retrieved 5 May 2014.
  34. ^ "Time Tree".
  35. ^ "NCBI Nucleotide: XP_002815448". Retrieved 18 May 2014.
  36. ^ "NCBI Nucleotide: XP_002696496". Retrieved 18 May 2014.
  37. ^ "NCBI Nucleotide: NP_034703". Retrieved 18 May 2014.
  38. ^ "NCBI Nucleotide: NP_001100801". Retrieved 18 May 2014.
  39. ^ "NCBI Nucleotide: NP_001025509". Retrieved 18 May 2014.
  40. ^ "NCBI Nucleotide: NP_001188351". Retrieved 18 May 2014.
  41. ^ "NCBI Nucleotide: XP_006002089". Retrieved 18 May 2014.
  42. ^ "NCBI Nucleotide: NP_997067". Retrieved 18 May 2014.
  43. ^ "NCBI Nucleotide: XP_002189063". Retrieved 18 May 2014.
  44. ^ "NCBI Nucleotide: XP_007254591.1". Retrieved 18 May 2014.
  45. ^ "NCBI Nucleotide: ETE68928". Retrieved 18 May 2014.
  46. ^ "NCBI Nucleotide: XP_004017207". Retrieved 18 May 2014.
  47. ^ "NCBI Nucleotide: XP_004678440". Retrieved 18 May 2014.
  48. ^ "NCBI Nucleotide: ACF10237.1". Retrieved 18 May 2014.
  49. ^ "NCBI Nucleotide: NP_001123285". Retrieved 18 May 2014.
  50. ^ "UniProt: F1KXE6". Retrieved 18 May 2014.
  51. ^ "NCBI Nucleotide: NP_492533.2". Retrieved 18 May 2014.
  52. ^ "NCBI Nucleotide: NP_524045". Retrieved 18 May 2014.

Further reading

This article incorporates text from the United States National Library of Medicine, which is in the public domain.

Retrieved from "https://en.wikipedia.org/w/index.php?title=IRX1&oldid=1212574088"
This page is based on the copyrighted Wikipedia article: IRX1. Articles is available under the CC BY-SA 3.0 license; additional terms may apply.Privacy Policy